Snapping doesn't seem to work on multiple objects
I happen to be on the same tutorial (I don't know how he doesn't have the same problem). I played around with it for a bit, and I found that, after duplicating all the blocks, selecting an odd number of columns/columnless tiles seems to remove the problem. Just select different numbers of blocks until it snaps properly and you should be fine.
If worse comes to worst, just move the blocks individually, it's not as big of a headache compared to doing the same thing with vertices.
P.S. Don't forget to add the roof spacing blocks.